Original Papers

• 1.

  Yuan, C., Rao, R.P., Jesmin, N., Bamba, T., Nagashima, K., Pascual, A., Preat, T., Fukusaki, E., Acharya, U. and Acharya, J.K.
  (2011) CDase is a pan-ceramidase in Drosophila.
  Mol. Biol. Cell. 22, 33-43.

• 2.

  Daikoku, S., Ono, Y., Ohtake, A., Hasegawa, Y., Fukusaki, E., Suzuki, K., Ito, Y., Goto, S. and Kanie, O.
  (2011) Fluorescence-monitored zero dead-volume nanoLC-microESI-QIT-TOF MS for analysis of fluorescently tagged glycosphingolipids.
  Analyst. 136,1046-1050.

• 3.

  Bando, K., Kunimatsu, T., Sakai, J., Kimura, J., Funabashi, H., Seki, T., Bamba, T. and Fukusaki, E
  (2011) GC-MS-based metabolomics reveals mechanism of action for hydrazine induced hepatotoxicity in rats.
  J. Appl. Toxicol., 31, 524-535.

• 4.

  Yonamine, I., Bamba, T., Nirala, N.K., Jesmin, N., Kosakowska-Cholody, T., Nagashima, K., Fukusaki, E., Acharya, J.K. and Acharya, U.
  (2011) Sphingosine kinases and their metabolites modulate endolysosomal trafficking in photoreceptors.
  J. Cell. Biol. 192, 557-567.

• 5.

  Kamei, Y., Tamura, T., Yoshida, R., Ohta, S., Fukusaki, E. and Mukai, Y.
  (2011) GABA metabolism pathway genes, UGA1 and GAD1, regulate replicative lifespan in Saccharomyces cerevisiae.
  Biochem. Biophys. Res. Commun. 407,185-190.

• 6.

  Hori, S., Nishiumi, S., Kobayashi, K., Shinohara, M., Hatakeyama, Y., Kotani, Y., Hatano, N., Maniwa, Y., Nishio, W., Bamba, T., Fukusaki, E., Azuma, T., Takenawa, T., Nishimura, Y. and Yoshida, M.A.
  (2011) A metabolomic approach to lung cancer.
  Lung Cancer. 74, 284-292.

• 7.

  Tsugawa, H., Tsujimoto, Y., Arita, M., Bamba, T. and Fukusaki, E.
  (2011) GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA).
  BMC Bioinformatics. 12,131-.

• 8.

  Hayashi, S., Yoshida, M., Fujiwara, T., Maegawa, S. and Fukusaki, E.
  (2011) Single-embryo metabolomics and systematic prediction of developmental stage in zebrafish.
  Z. Naturforsch. C. 66,191-198.

• 9.

  Ono, D., Bamba, T., Oku, Y., Yonetan,i T. and Fukusaki, E.
  (2011) Application of Fourier transform near-infrared spectroscopy to optimization of green tea steaming process conditions.
  J. Biosci. Bioeng. 112, 247-251.

• 10.

  Tsugawa, H., Bamba, T., Shinohara, M., Nishiumi, S., Yoshida, M. and Fukusaki, E.
  (2011) Practical non-targeted gas chromatography/mass spectrometry-based metabolomics platform for metabolic phenotype analysis.
  J. Biosci. Bioeng. 112, 292-298.

• 11.

  Shima, N., Miyawaki, I., Bando, K., Horie, H., Zaitsu, K., Katagi, M., Bamba, T., Tsuchihashi, H. and Fukusaki, E.
  (2011) Influences of methamphetamine-induced acute intoxication on urinary and plasma metabolic profiles in the rat.
  Toxicology. 287, 29-37.

• 12.

  Jumtee, K., Komura, H., Bamba, T. and Fukusaki, E.
  (2011) Predication of Japanese green tea (Sen-cha) ranking by volatile profiling using gas chromatography mass spectrometry and multivariate analysis.
  J. Biosci. Bioeng. 112, 252-255.

• 13.

  Okazawa, A., Hori, K., Okumura, R., Izumi, Y., Hata, N., Bamba, T., Fukusaki, E., Ono, E., Satake, H. and Kobayashi, A.
  (2011) Simultaneous quantification of lignans in Arabidopsis thaliana by highly sensitive capillary liquid chromatography-electrospray ionization-ion trap mass spectrometry.
  Plant Biotechnology, 28, 287-293.

• 14.

  Wada, Y., Matsubara, A., Uchikata, T., Iwasaki, Y., Morimoto, S., Kan, K., Okura, T., Fukusaki, E. and Bamba T.
  (2011) Metabolic profiling of β-cryptoxanthin and its fatty acid esters by supercritical fluid chromatography coupled with triple quadrupole mass spectrometry.
  J. Sep. Sci. 34, 3546-52.

• 15.

  Lee, J.W., Yamamoto, T., Uchikata, T., Matsubara, A., Fukusaki, E. and Bamba, T.
  (2011) Development of a polar lipid profiling method by supercritical fluid chromatography/mass spectrometry.
  J. Sep. Sci. 34, 3553-3560.

• 16.

  Sugimoto, T., Bamba, T., Izumi, Y., Nomura, H., Shiina, T. and Fukusaki, E.
  (2011) Use of ultra-performance liquid chromatography/time-of-flight mass spectrometry with nozzle-skimmer fragmentation for comprehensive quantitative analysis of secondary metabolites in Arabidopsis thaliana.
  J. Sep. Sci. 34, 3587-3596.

Reviews

• 1.

  Katoh, A., Fukuda, S., Fukusaki, E., Hashimoto, T., Hayasaki, T., Kanaya, S., Komura, H., Nomoto, K., Shojo, M. and Takeno, K.J.
  (2011) Systems biology in a commercial quality study of the Japanese angelica radix: toward an understanding of traditional medicinal plants.
  Am. J. Chin. Med. 39, 757-777.

Original Papers

• 1.

  Ojima, Y., Ashida, T., Kusuda, A., Kino-oka, M. and Taya, M.
  (2011) Evaluation index of cellular states accompanying the life-span progression of human ketatinocytes.
  KAGAKU KOGAKU RONBUNSHU 37, 351-355

• 2.

  Katakura, Y., Moukamnerd, C., Harashima, S. and Kino-oka, M.
  (2011) Strategy for preventing bacterial contamination by adding exogenous ethanol in solid-state semi-continuous bioethanol production.
  J. Biosci. Bioeng. 111, 343-345.

• 3.

  Kim, M.-H., Tsubakino, N., Kagita, S., Taya, M. and Kino-oka, M.
  (2011) Characterization of spatial cell distribution in multilayer sheet of human keratinocytes through a stereoscopic cell Imaging system.
  J. Biosci. Bioeng. 112, 289-291.

• 4.

  Nadzir, M.M., Kino-oka, M., Maruyama, N., Sato, Y., Kim, M.-H., Sugawara, K. and Taya, M.
  (2011) Comprehension of terminal differentiation and dedifferentiation of chondrocytes during passage cultures.
  J. Biosci. Bioeng. 112, 395-401.

• 5.

  Mashayekhan, S., Kim, M.-H., Kino-oka , M., Miyazaki, J. and Taya, M.
  (2011) Embryonic stem cells maintain an undifferentiated state on dendrimer-immobilized surface with d-glucose display.
  Polymers 3, 2078-2087.

Original Papers

• 1.

  Khemkladngoen, N., Cartagena, J., Shibagaki, N. and Fukui, K.
  (2011) Adventitious shootregeneration from juvenile cotyledons of a biodiesel producing Plant, Jatrophacurcas L.
  J Biosci Bioeng. 111, 67-70.

• 2.

  Amano, M., Hasegawa, J., Kobayashi, N., Kishi, N., Nakazawa, T., Uchiyama, S. and Fukui, K.
  (2011) Specific racemization of heavy-chain cysteine-220 in the hinge region of immunoglobulin gamma 1 as a possible cause of degradation during storage.
  Anal. Chem. 15, 3857-3864.

• 3.

  Kurihara, D., Matsunaga, S., Omura, T., Higashiyama, T. and Fukui, K..
  (2011) Identification and characterization of plant Haspin kinase as a histone H3 threonine kinase.
  BMC Plant Biol. 11, 73

• 4.

  Noda, M., Uchiyama, S., McKay, A.R. Morimoto, A., Misawa, S., Yoshida, A., Shimahara, H., Takinowaki, H., Nakamura, S., Kobayashi, Y., Matsunaga, S., Ohkubo, T., Robinson, C.V., and Fukui K.
  (2011) Assembly states of the nucleosome assembly protein 1 (NAP-1) revealed by sedimentation velocity and non-denaturing mass spectrometry.
  Biochemical Journal 436, 101-112.

• 5.

  Sakamoto, T., Inui, YT., Uraguchi, S., Yoshizumi, T., Matsunaga, S., Mastui, M., Umeda, M., Fukui, K. and Fujiwara T.
  (2011) Condensin II alleviates DNA damage and is essential for tolerance of boron overload stress in Arabidopsis.
  Plant Cell 23, 3533-3546

• 6.

  Nishi, N., Miyajima, M., Wakiyama, N., Kubota, K., Hasegawa, J., Uchiyama, S. and Fukui, K.
  (2011) Fc domain mediated self-association of an IgG1 monoclonal antibody under a low ionic strength condition.
  J. Biosci. Bioeng. 112,326-332.

• 7.

  Lee, MH., Lin, L., Equilibrina, I., Uchiyama, S., Matsunaga, S., and Fukui, K.
  (2011) ASURA (PHB2) Is Required for Kinetochore Assembly and Subsequent Chromosome Congression.
  Acta Histochem Cytochem. 44, 247-258.

Original Papers

• 1.

  Caschera, F., Sunami, T., Matsuura, T., Suzuki, H., Hanczyc, M. and Yomo, T.
  (2011) Programmed Vesicle Fusion Triggers Gene Expression.
  Langmuir 27(21), 13082-90.

• 2.

  Matsuura, T., Hosoda, K., Ichihashi, N., Kazuta, Y. and Yomo, T.
  (2011) Kinetic analysis of beta-galactosidase and beta-glucuronidase tetramerization coupled with protein translation.
  J Biol Chem 286, 22028-34.

• 3.

  Kato, Y., Shiga, Y., Kobayashi, K., Tokishita, S., Yamagata, H., Iguchi, T. and Watanabe, H.
  (2011) Development of an RNA interference method in the cladoceran crustacean Daphnia magna.
  Dev Genes Evol 220, 337-345.

• 4.

  Yanagida, H., Matsuura, T., Kazuta, Y. and Yomo, T.
  (2011) In Vitro Selection of Proteins that Undergo Covalent Labeling with Small Morecules by Thiol-Disulfide Exchange by Using Ribosome Display.
  Chembiochem 12, 962-9.

• 5.

  Kato, Y., Kobayashi, K., Watanabe, H. and Iguchi, T.
  (2011) Environmental Sex Determination in the Branchiopod Crustacean Daphinia magna: Deep Conservation of a Doublesex Gene in the Sex-Determining Pathway.
  Plos Genet7(3):e1001345.

• 6.

  Hosoda, K., Matsuura, T., Suzuki, H. and Yomo, T.
  (2011) Origin of Longnormal-like distributions with a common width in a growth and division process.
  Physical Review E 83, 031118.

Reviews

• 1.

  Matsuura, T., Ichihashi, N., Sunami, T., Kita, H., Suzuki, H. and Yomo, T.
  (2011) Evolvability and Self-Replication of Genetic Information in Liposomes.
  In The Minimal Cell (Luisi, P.L. & Stano, P., eds.), pp. 275-287. Springer Netherlands.

Original Papers

• 1.

  Morimoto, K., Ono, E., Kim, H.-J., Okazawa, A., Kobayashi, A. and Satake, H.
  (2011) The construction of transgenic Forsythia plants: comparative study of three Forsythia species.
  Plant Biotechnol. 28, 273-280.

• 2.

  Okazawa, A., Hori, K., Okumura, R., Izumi, Y., Hata, N., Bamba, T., Fukusaki, E., Ono, E., Satake, H. and Kobayashi, A.
  (2011) Simultaneous quantification of lignans in Arabidopsis thaliana by highly sensitive capillary liquid chromatography-electrospray ionization-ion trap mass spectrometry.
  Plant Biotechnol. 28, 287-293.

• 3.

  Morimoto, K., Kim, H.-J., Ono, E., Kobayashi, A., Okazawa, A. and Honoo, S.
  (2011) Effects of light on production of endogenous and exogenous lignans by Forsythia koreana wildtype and transgenic cells.
  Plant Biotechnol. 28, 331-337.

• 4.

  Seki, H., Sawai, S., Ohyama, K., Mizutani, M., Ohnishi, T., Sudo, H., Fukushima, E.O., Akashi, T., Aoki, T., Saito, K. and Muranaka, T.
  (2011) Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin.
  Plant Cell 23, 4112-4123.

• 5.

  Tang, J., Ohyama, K., Kawaura, K., Hashinokuchi, H., Kamiya, Y., Suzuki, M., Muranaka, T. and Ogihara, Y.
  (2011) A new insight into application for barley chromosome addition lines of common wheat: achievement of stigmasterol accumulation.
  Plant Physiol. 157, 1555-1567.

• 6.

  Fukushima, E.O., Seki, H., Ohyama, K., Ono, E., Umemoto, N., Mizutani, M., Saito, K. and Muranaka, T.
  (2011) CYP716A subfamily members are multifunctional oxidases in triterpenoid biosynthesis.
  Plant Cell Physiol. 52, 2050-2061.

Reviews

• 1.

  Muranaka, T.
  (2011) Plant gateway vectors for RNAi as a tool for functional genomic studies.
  Methods Mol. Biol. 744, 27-35.

Original Papers

• 1.

  Cappelletti, M., Fedi, S., Frascari, D., Ohtake, H., Turner, R.J. and Zannoni, D.
  (2011) Analyses of both the alkB gene transcriptional start site and alkB promoter inducing properties in Rhodococcus sp. BCP1 as grown on n-alkanes.
  Appl. Environ. Microb iol. 77, 1619-1627

• 2.

  Soh, Z. Tsuji, T., Takiguchi, N. and Ohtake, H.
  (2011) An artificial neural network approach for glomerular activity pattern prediction using the graph kernel method and the Gaussian mixture functions.
  Chem. Senses 36, 413-424

• 3.

  Izawa, N., Serata, M., Sone, T., Omasa, T., and Ohtake, H.
  (2011) Hyaluronic acid production by recombinant Streptococcus thermophilus.
  J. Biosc. Bioeng. 111, 665-670

• 4.

  Kang, B.-M., Honda, K., Okano, K., Aki, T., Omasa, T. and Ohtake, H.
  (2011) Thermal analysis for differentiating between oleaginous and non-oleaginous microorganisms.
  Biochem. Eng. J. 57, 23-29

• 5.

  Motomura, K., Hirota, R., Ohnaka, N., Okada, M., Ikeda, T., Morohoshi, M., Ohtake, H. and Kuroda, K.
  (2011) Overproduction of YjbB reduces the level of polyphosphate in Escherichia coli : a hypothetical role of YjbB in phosphate export and polyphosphate accumulation.
  FEMS Microbiol. Lett. 320, 25-32

• 6.

  Restiawaty, E., Iwasa, Y., Maya, S., Honda, K., Omasa, T., Hirota, R., Kuroda, A. and Ohtake, H.
  (2011) Feasibility of thermophilic adenosine triphosphate-regeneration system using Thermusthermophilus polyphosphate kinase.
  Process Biochem. 46, 1747-1752

• 7.

  Kang, B.-M., Honda, K., Aki, T., Omasa, T. and Ohtake, H.
  (2011) Simultaneous thermogravimetry and differential thermal analysis for comparing burning characteristics between oleaginous and non-oleaginous microorganisms.
  Thermochim. Acta 517, 115-120.

Original Papers

• 1.

  Sugiyama, M., Nugroho, S., Iida, N., Sakai, T., Kaneko, Y. and Harashima, S.
  (2011) Genetic interactions of ribosome maturation factors Yvh1 and Mrt4 influence mRNA decay, glycogen accumulation, and the expression of early meiotic genes in Saccharomyces cerevisiae.
  J. Biochem. 150, 103-11.

• 2.

  Chuwattanakul, V., Kim, Y., Sugiyama, M., Nishiuchi, H. Miwa, H., Kaneko, Y. and Harashima, S.
  (2011) Construction of a Saccharomyces cerevisiae strain with a high level of RNA.
  J. Biosci. Bioeng. 112, 1-7.

• 3.

  Prasetyo, J., Naruse, K., Kato, T., Boonchird, C., Harashima S. and Park, Y., E.
  (2011) Bio-conversion of paper sludge to biofuel by simultaneous saccharification and fermentation using a cellulase of paper sludge origin and thermotolerant Saccharomyces cerevisiae TJ14.
  Biotechnol. Biofuels 4, 35.

• 4.

  Akao, T., Yashiro, I., Hosoyama, A., Kitagaki, H., Horikawa, H., Watanabe, D., Akada, R., Ando, Y., Harashima S., Inoue, T., Inoue, Y., Kajiwara, S., Kitamoto, K., Kitamoto, N., Kobayashi, O., Kuhara, S., Masubuchi, T., Mizoguchi, H., Nakao, Y., Nakazato A., Namise, S., Oba, T., Ogata, T., Ohta A., Sato, M., Shibasaki, S., Takatsume, Y., Tanimoto, S., Tsuboi, H., Yamashita, N., Yoda, K., Ishikawa, T., Iwashita, K., Fujita, N. and Shimoi, H.
  (2011) Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7.
  DNA Res. 18, 423-434.

• 5.

  Shahsavarani, H., Sugiyama, M., Kaneko, Y., Chuenchit, B. and Harashima, S.
  (2011) Superior thermotolerance of Saccharomyces cerevisiae for efficient bioethanol fermentation can be achieved by overexpression of RSP5 ubiquitin ligase.
  Biotechnol. Adv. 30, 1289-300.

• 6.

  Ueda, Y., Ikushima, S., Sugiyama, M., Matoba, R., Kaneko, Y., Matsubara, K. and Harashima, S.
  (2012) Large-scale genome reorganization in Saccharomyces cerevisiae through combinatorial loss of mini-chromosomes.
  J. Biosci. Bioeng. 113, 675-82.

Original Papers

• 1.

  Sato, A., Yokotani, A., Tadokoro, T., Tanaka, S., Angkawidjaja, C., Koga, Y., Takano, K. and Kanaya, S.
  (2011) Crystal structure of stable protein, CutA1, from a psychrotrophic bacterium Shewanella sp. SIB1.
  J. Synchrotron Rad. 18, 6-10.

• 2.

  Kim, J-J., Jin, H.M., Lee, H.J., Jeon, C.O., Kanaya, E., Koga, Y., Takano, K. and Kanaya, S.
  (2011) Flavobacterium banpakuense sp. nov. isolated from leaf-and-branch compost.
  Int. J. Syst. Evol. Microbiol. 61, 1595-1600.

• 3.

  Iefuji, N., Murai, R., Maruyama, M., Takahashi, Y., Sugiyama, S., Adachi, H., Matsumura, H., Murakami, S., Inoue, T., Mori, Y., Koga, Y., Takano, K. and Kanaya, S.
  (2011) Laser-induced nucleation in protein crystallization: local increase in protein concentration induced by femtosecond laser irradiation.
  J. Cryst. Growth. 318, 741-744.

• 4.

  Tanaka, S., Koga, Y., Takano, K. and Kanaya, S.
  (2011) Inhibition of chymotrypsin- and subtilisin-like serine proteases with Tk-serpin from hyperthermophilic archaeon Thermococcus kodakaraensis.
  Biochim. Biophys. Acta 1814, 299-307.

• 5.

  Kuwahara, K., Angkawidjaja, C., Koga, Y., Takano, K., and Kanaya, S.
  (2011) Importance of an extreme C-terminal motif of a family I.3 lipase for stability.
  Protein Eng. Des. Sel. 24, 411-418.

• 6.

  Takano, K., Okamoto, T., Okada, J., Tanaka, S., Angkawidjaja, C., Koga, Y. and Kanaya, S.
  (2011) Stabilization by fusion to the C-terminus of hyperthermophile Sulfolobus tokodaii RNase HI: a possibility of protein stabilization tag.
  PLoS ONE 6, e16226.

• 7.

  Tayyab, M, Rashid, N., Angkawidjaja, C., Kanaya, S. and Akhtar, M.
  (2011) Highly active metallocarboxypeptidase from newly isolated Geobacillus strain SBS-4S: cloning and characterization.
  J. Biosci. Bioeng. 111, 259-265.

• 8.

  Sinsereekul, N., Foophow, T., Yamanouchi, M., Koga, Y., Takano, K. and Kanaya, S.
  (2011) An alternative mature form of subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis identified in the presence of Ca2+.
  FEBS J. 278, 1901-1911.

• 9.

  Matsumura, H., Sugiyama, S., Hirose, M., Kakinouchi, K., Maruyama, M., Murai, R., Adachi, H., Takano, K., Murakami, S., Mori, Y. and Inoue, T.
  (2011) Approach for growth of high-quality and large protein crystals.
  J. Synchrotron Rad. 18, 16-19.

• 10.

  Sugiyama, S., Hirose, M., Shimizu, N., Niiyama, M., Maruyama, M., Sazaki, G., Murai, R., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y. and Matsumura, H.
  (2011) Effect of evaporation on protein crystals grown in semi-solid agarose hydrogel.
  Jpn. J. Appl. Phys. 50, 025502.

• 11.

  Miyashita, S., Tadokoro, T., Angkawidjaja, C., You, D-J., Koga, Y., Takano, K. and Kanaya, S.
  (2011) Identification of the substrate binding site in the N-terminal TBP-like domain of RNase H3.
  FEBS Lett. 585, 2313-2317.

• 12.

  Budiman, C., Angkawidjaja, C., Motoike, H., Koga, Y., Takano, K. and Kanaya, S.
  (2011) Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: dimer dissociation by disruption of Val-Leu knot.
  Protein Sci. 20, 1755-1764.

Reviews

• 1.

  Budiman, C., Koga, Y., Takano, K. and Kanaya, S.
  (2011) FK506-binding protein 22 from a psychrotrophic bacterium, a cold shock-inducible peptidyl prolyl isomerase with the ability to assist in protein folding.
  Int. J. Mol. Sci. 12, 5261-5284.

• 2.

  Mukaiyama, A. and Takano, K.
  (2011) Folding and unfolding of hyperthermophilic proteins; molecular basis of adaptation to hot environment.
  Protein Folding (E. C. Walters, ed.), pp. 443-464. Nova Science, Hauppauge (NY).

Original Papers

• 1.

  Dohi, K., Isoyama-Tanaka, J., Misaki, R. and Fujiyama, K.
  (2011) Jack bean α-mannosidase digestion profile of hybrid-type N-glycans: effect of reaction pH on substrate preference.
  Biochimie. 93, 766-71.

• 2.

  Kajiura, H., Misaki, R., Fujiyama K. and Seki, T.
  (2011) Stable coexpression of two human sialylation enzymes in plant suspension-cultured tobacco cells.
  J Biosci Bioeng. 111, 471-7.

• 3.

  Isoyama-Tanaka, J., Dohi, K., Misaki, R. and Fujiyama, K.
  (2011) Improved expression and characterization of recombinant human Golgi α1,2-mannosidase I isoforms (IA2 and IC) by Escherichia coli.
  J Biosci Bioeng. 112, 14-9.

• 4.

  Kaulfürst-Soboll, H., Rips, S., Koiwa, H., Kajiura, H., Fujiyama, K. and von Schaewen, A.
  (2011) Reduced immunogenicity of Arabidopsis hgl1 mutant N-glycans caused by altered accessibility of xylose and core fucose epitopes.
  J Biol Chem. 286, 22955-64.

• 5.

  Kimura, Y., Takeoka, Y., Inoue, M., Maeda, M. and Fujiyama, K.
  (2011) Double-knockout of putative endo-β-N-acetylglucosaminidase (ENGase) genes in Arabidopsis thaliana: loss of ENGase activity induced accumulation of high-mannose type free N-glycans bearing N,N'-acetylchitobiosyl unit.
  Biosci Biotechnol Biochem 75, 1019-21.

• 6.

  Misaki, R., Sakai, Y., Omasa, T. and Fujiyama, K. and Seki, T.
  (2011) N-terminal vacuolar sorting signal at the mouse antibody alters the N-linked glycosylation pattern in suspension-cultured tobacco BY2 cells.
  J Biosci Bioeng. 112, 476-84.

Original Papers

• 1.

  Kitani, S., Miyamoto, K.T., Takamatsu, S., Herawati, E., Iguchi, H., Nishitomi, K., Uchida, M., Nagamitsu, T., Omura, S., Ikeda, H. and Nihira, T.
  (2011) Avenolide, a Streptomyces hormone controlling antibiotic production in Streptomyces avermitilis.
  Proc. Natl. Acad. Sci. U. S. A. 108, 16410-16415.

• 2.

  Uchida, M., Takamatsu, S., Arima, S., Miyamoto, K.T., Kitani, S., Nihira, T., Ikeda, H. and Nagamitsu, T.
  (2011) Total synthesis and absolute configuration of avenolide, extracellular factor in Streptomyces avermitilis.
  J. Antibiot. (Tokyo) 64,781-787.

• 3.

  Ningsih, F., Kitani, S., Fukushima, E. and Nihira, T.
  (2011) VisG is essential for biosynthesis of virginiamycin S, a streptogramin type B antibiotic, as a provider of the nonproteinogenic amino acid phenylglycine.
  Microbiology 157, 3213-3220.

• 4.

  Miyamoto, K.T., Kitani, S., Komatsu, M., Ikeda, H. and Nihira, T.
  (2011) The autoregulator-receptor homologue AvaR3 plays a regulatory role in antibiotic production, mycelial aggregation and colony development of Streptomyces avermitilis.
  Microbiology 157, 2266-2275.

• 5.

  Intra, B., Mungsuntisuk, I., Nihira, T., Igarashi, Y. and Panbangred, W.
  (2011) Identification of actinomycetes from plant rhizospheric soils with inhibitory activity against Colletotrichum spp., the causative agent of anthracnose disease.
  BMC. Res. Notes. 4, 98.

• 6.

  Siriwach, R., Kinoshita, H., Kitani, S., Igarashi, Y., Pansuksan, K., Panbangred, W. and Nihira T.
  (2011) Xylaropyrone, a new γ-pyrone from the endophytic fungus Xylaria feejeensis MU18.
  J. Antibiot. (Tokyo) 64, 217-219.

Original Papers

• 1.

  Nakano, M., Imamura, H., Nagai, T. and Noji, H.
  (2011) Ca2+ regulation of mitochondrial ATP synthesis visualized at the single cell level.
  ACS Chem Biol. 6, 709-715.

• 2.

  Nomura, M., Nagai, T., Harada, Y. and Tani, T.
  (2011) Facilitated intracellular transport of TrkA by an interaction with nerve growth factor.
  Dev Neurobiol. 71, 634-649.

• 3.

  Yamada, Y., Michikawa, T., Hashimoto, M., Horikawa, K., Nagai, T., Miyawaki, A., Häusser, M. and Mikoshiba, K.
  (2011) Quantitative Comparison of Genetically Encoded Ca2+ Indicators in Cortical Pyramidal Cells and Cerebellar Purkinje Cells.
  Front Cell Neurosci. 5, 18(1-10).

• 4.

  Zhao, Y., Araki, S., Wu, J., Teramoto, T., Chang, YF., Nakano, M., Abdelfattah, AS., Fujiwara, M., Ishihara, T., Nagai T. and Campbell, RE.
  (2011) An expanded palette of genetically encoded Ca²+ indicators.
  Science 333, 1888-1891.

• 5.

  Saito, K., Arai, Y., Zhang, J., Kobayashi, K., Tani, T. and Nagai, T.
  (2011) Conjugation of both on-axis and off-axis light in Nipkow disk confocal microscope to increase availability of incoherent light source.
  Cell Struct Funct. 36, 237-246.

• 6.

  Kwon, HJ., Ohmiya, Y., Honma, KI., Honma, S., Nagai, T., Saito, K. and Yasuda, K.
  (2012) Synchronized ATP oscillations have a critical role in prechondrogenic condensation during chondrogenesis.
  Cell Death Dis. 3, e278.

Original Papers

• 1.

  Yoshikawa, K., Tanaka, T., Ida, Y., Furusawa, C., Hirasawa, T. and Shimizu, H.
  (2011) Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae.
  Yeast 28, 349-361.

• 2.

  Suzuki, S., Ono, N., Furusawa, C., Ying, B-W. and Yomo, T.
  (2011) Comparison of sequence reads obtained from three
  next-generation sequencing platforms.
  PLoS One 6, e19534.

• 3.

  Kim, J., Hirasawa, T., Saito, M., Furusawa, C. and Shimizu, H.
  (2011) Investigation of phosphorylation status of OdhI protein during penicillin- and Tween 40-triggered glutamate overproduction by Corynebacterium glutamicum.
  Appl. Microbiol. Biotechnol. 91, 143-151.

• 4.

  Matsuda, F., Furusawa, C., Kondo, T., Ishii, J., Shimizu, H. and Kondo, A.
  (2011) Engineering strategy of yeast metabolism for higher alcohol production.
  Microbial Cell Factories. 10, 70.

• 5.

  Umakoshi, M., Hirasawa, T., Furusawa, C., Takenaka, Y., Kikuchi, Y. and Shimizu, H.
  (2011) Improving protein secretion of a transglutaminase-secreting
  Corynebacterium glutamicum recombinant strain on the basis of 13C metabolic flux analysis.
  J. Biosci. Bioeng. 112, 595-601.

• 6.

  Yoshikawa, K., Kojima, Y., Nakajima, T., Furusawa, C., Hirasawa T. and Shimizu, H.
  (2011) Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp.
  Appl. Microbiol. Biotechnol. 92, 347-358.

• 7.

  Mori, E., Furusawa, C., Kajihata, S., Shirai, T. and Shimizu, H.
  (2011) Evaluating 13C enrichment data of free amino acids for precise metabolic flux analysis.
  Biotechnol. J. 6, 1377-1378.

Original Papers

• 1.

  Mori, K., Kashiwagi, A. and Yomo, T.
  (2011) Single-Cell Isolation and Cloning of Tetrahymena thermophila Cells with a Fluorescence-Activated Cell Sorter.
  J Eukaryot Microbiol. 58, 37-42.

• 2.

  Hosoda, K., Suzuki, S., Yamauchi, Y., Shiroguchi, Y., Kashiwagi, A., Ono, N., Mori, K. and Yomo, T.
  (2011) Cooperative adaptation to establishment of a synthetic bacterial mutualism.
  PLoS One 6, e17105.

• 3.

  Kihara, K., Mori, K., Suzuki, S., Hosoda, K., Yamada, A., Matsuyama, S., Kashiwagi, A. and Yomo, T.
  (2011) Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli.
  Biosystems 103, 342-347.

• 4.

  Hosoda, K., Matsuura, T., Suzuki, H. and Yomo, T.
  (2011) Origin of lognormal-like distributions with a common width in a growth and division process.
  Phys Rev E Stat Nonlin Soft Matter Phys. 83, e031118.

• 5.

  Yanagida, H., Matsuura, T., Kazuta, Y. and Yomo, T.
  (2011) In vitro selection of proteins that undergo covalent labeling with small molecules via thiol-disulfide exchange using ribosome display.
  Chembiochem. 12, 962-969.

• 6.

  Suzuki, S., Ono, N., Furusawa, C., Ying, B. and Yomo, T.
  (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms.
  PLoS One 6, e19534.

• 7.

  Tsuru, S., Yasuda, N., Murakami, Y., Ushioda, J., Kashiwagi, A., Suzuki, S., Mori, K., Ying, B. and Yomo, T.
  (2011) Adaption by stochastic switching of a monostable genetic circuit in Escherichia coil.
  Mol Syst Biol. 7, 1-10.

• 8.

  Matsuura, T., Hosoda, K., Ichihashi, N., Kazuta, Y. and Yomo, T.
  (2011) Kinetic Analysis of -Galactosidase and -Glucuronidase Tetramerization Coupled with Protein Translation.
  J Biol Chem. 286, 22028-22034.

• 9.

  Kashiwagi, A. and Yomo, T.
  (2011) Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Qβ and Escherichia coli.
  PLoS Genet 7, e1002188.

• 10.

  Shimizu, Y., Tsuru, S., Ito, Y., Ying, B. and Yomo, T.
  (2011) Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population.
  PLoS One 6, e23953.

• 11.

  Caschera, F., Sunami, T., Matsuura, T., Suzuki, H., Hanczyc, M. and Yomo, T.
  (2011) Programmed Vesicle Fusion Triggers Gene Expression.
  Langmuir 27, 13082-13090.

• 12.

  Matsumoto, Y., Ito, Y., Tsuru, S., Ying, B. and Yomo, T.
  (2011) Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation.
  J Biomed Biotechnol. 2011, 1-10.

• 13.

  Ichii, T., Suzuki, H. and Yomo, T.
  (2011) Micro-droplet model for recursive growth and division dynamics of the cell.
  EPL. 96, e48006.

• 14.

  Hosoda, K. and Yomo, T.
  (2011) Designing symbiosis.
  Bioeng Bugs. 2, 338-341